Well, the root folder means the beginning of a folder structure. So for SH3 this means where it is installed. By default: C:\Program Files\Ubisoft\SilentHunterIII\
SH3 has it's executable stored in there, but some applications or games have the executable file stored in a subfolder (like \bin). So it is not always true that the root folder contains the executable program.
Similarly, the root of the harddisk would be C:\. And the root of the Windows folderstructure is then c:\Windows
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